# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:07:06 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-(5-methylfuran-2-carbonyl)-N-[(pyridin-3-yl)methyl]piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(cc1)C(=O)N2CCN(CC2)C(=O)NCc3cccnc3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 Y47  Y47  4-(5-methylfuran-2-carbonyl)-N-[(pyridin-3-yl)methyl]piperazine-1-carboxamide  ligand  44  24  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y47
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 Y47  N1   N  NT    0  -0.470  -18.8563  13.1048  25.4462
 Y47  N3   N  NH1   0  -0.685  -15.3149  16.6315  25.6392
 Y47  C4   C  CR15  0  -0.298  -22.3640  11.9347  25.6236
 Y47  C5   C  CR5   0   0.198  -21.2424  12.6949  25.7188
 Y47  C6   C  C     0   0.483  -20.0053  12.6244  24.9209
 Y47  C7   C  CH2   0  -0.309  -17.6912  13.3169  24.6152
 Y47  C8   C  CH2   0  -0.310  -17.1911  14.7468  24.7718
 Y47  C10  C  CH2   0  -0.367  -14.4683  17.7448  25.9979
 Y47  C13  C  CR16  0  -0.317  -15.6829  20.9024  27.7193
 Y47  C15  C  CR16  0  -0.089  -16.2128  19.4915  25.4739
 Y47  C17  C  CH2   0  -0.329  -18.5473  13.3345  26.8447
 Y47  C11  C  CR6   0   0.028  -15.2265  19.0066  26.3280
 Y47  C12  C  CR16  0  -0.193  -14.9662  19.7404  27.4761
 Y47  C14  C  CR16  0  -0.076  -16.6430  21.2902  26.7987
 Y47  C16  C  CH2   0  -0.276  -18.0984  14.7663  27.0537
 Y47  C2   C  CR5   0   0.367  -22.6757  13.5349  27.1429
 Y47  C3   C  CR15  0  -0.377  -23.2904  12.4732  26.5565
 Y47  C9   C  C     0   0.758  -16.1326  16.0816  26.5783
 Y47  N2   N  NT    0  -0.515  -16.9893  15.0900  26.1689
 Y47  N4   N  N     0  -0.399  -16.9072  20.5996  25.6945
 Y47  O1   O  O     0  -0.475  -20.0717  12.1491  23.7936
 Y47  O2   O  O     0  -0.529  -16.0711  16.4400  27.7484
 Y47  O3   O  O     0  -0.428  -21.4349  13.6724  26.6370
 Y47  H10  H  HNH1  0   0.408  -15.4936  16.5053  24.6586
 Y47  H5   H  HCR5  0   0.268  -22.5081  11.0880  24.9723
 Y47  H6   H  HCH2  0   0.249  -16.9022  12.6149  24.9033
 Y47  H7   H  HCH2  0   0.277  -17.9327  13.1367  23.5713
 Y47  H9   H  HCH2  0   0.259  -16.2496  14.7997  24.2265
 Y47  H8   H  HCH2  0   0.242  -17.8993  15.4335  24.2923
 Y47  H11  H  HCH2  0   0.262  -13.8239  17.4751  26.8355
 Y47  H12  H  HCH2  0   0.274  -13.8085  17.9254  25.1478
 Y47  H14  H  HCR6  0   0.268  -15.5072  21.4937  28.6076
 Y47  H16  H  HCR6  0   0.254  -16.4569  18.9492  24.5647
 Y47  H20  H  HCH2  0   0.255  -17.7375  12.6529  27.1262
 Y47  H19  H  HCH2  0   0.280  -19.3873  13.1107  27.4924
 Y47  H3   H  HCH3  0   0.260  -23.0859  15.5309  27.7898
 Y47  H2   H  HCH3  0   0.261  -24.1277  14.2862  28.4786
 Y47  H1   H  HCH3  0   0.259  -22.4710  14.4705  29.0551
 Y47  H13  H  HCR6  0   0.265  -14.2128  19.4033  28.1782
 Y47  H15  H  HCR6  0   0.260  -17.2233  22.1924  26.9581
 Y47  H17  H  HCH2  0   0.266  -17.7821  14.8916  28.0855
 Y47  H18  H  HCH2  0   0.232  -18.9443  15.4418  26.8769
 Y47  H4   H  HCR5  0   0.265  -24.2878  12.1219  26.7662
 Y47  C1   C  CH3   0  -0.753  -23.1086  14.5082  28.1701

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 Y47  C1   C2   single    1.480  0.020  1.480
 Y47  C2   C3   aromatic  1.360  0.020  1.360
 Y47  C3   C4   aromatic  1.421  0.020  1.421
 Y47  C4   C5   aromatic  1.358  0.020  1.358
 Y47  C5   C6   single    1.474  0.020  1.474
 Y47  C6   O1   double    1.225  0.020  1.225
 Y47  C6   N1   single    1.352  0.020  1.352
 Y47  N1   C7   single    1.447  0.020  1.447
 Y47  C7   C8   single    1.523  0.020  1.523
 Y47  C8   N2   single    1.453  0.020  1.453
 Y47  N2   C9   single    1.373  0.020  1.373
 Y47  C9   O2   double    1.225  0.020  1.225
 Y47  C9   N3   single    1.361  0.020  1.361
 Y47  N3   C10  single    1.444  0.020  1.444
 Y47  C10  C11  single    1.509  0.020  1.509
 Y47  C11  C12  aromatic  1.387  0.020  1.387
 Y47  C12  C13  aromatic  1.387  0.020  1.387
 Y47  C13  C14  aromatic  1.386  0.020  1.386
 Y47  C14  N4   aromatic  1.329  0.020  1.329
 Y47  N4   C15  aromatic  1.326  0.020  1.326
 Y47  N2   C16  single    1.455  0.020  1.455
 Y47  C16  C17  single    1.515  0.020  1.515
 Y47  C5   O3   aromatic  1.355  0.020  1.355
 Y47  C2   O3   aromatic  1.347  0.020  1.347
 Y47  N1   C17  single    1.451  0.020  1.451
 Y47  C11  C15  aromatic  1.392  0.020  1.392
 Y47  N3   H10  single    0.890  0.020  1.040
 Y47  C4   H5   single    0.930  0.020  1.080
 Y47  C7   H6   single    0.970  0.020  1.090
 Y47  C7   H7   single    0.970  0.020  1.090
 Y47  C8   H9   single    0.970  0.020  1.090
 Y47  C8   H8   single    0.970  0.020  1.090
 Y47  C10  H11  single    0.970  0.020  1.090
 Y47  C10  H12  single    0.970  0.020  1.090
 Y47  C13  H14  single    0.930  0.020  1.080
 Y47  C15  H16  single    0.930  0.020  1.080
 Y47  C17  H20  single    0.970  0.020  1.090
 Y47  C17  H19  single    0.970  0.020  1.090
 Y47  C1   H3   single    0.970  0.020  1.090
 Y47  C1   H2   single    0.970  0.020  1.090
 Y47  C1   H1   single    0.970  0.020  1.090
 Y47  C12  H13  single    0.930  0.020  1.080
 Y47  C14  H15  single    0.930  0.020  1.080
 Y47  C16  H17  single    0.970  0.020  1.090
 Y47  C16  H18  single    0.970  0.020  1.090
 Y47  C3   H4   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 Y47  C17  N1   C7   111.04  3.000
 Y47  C17  N1   C6   127.74  3.000
 Y47  C7   N1   C6   120.90  3.000
 Y47  H10  N3   C9   121.05  3.000
 Y47  H10  N3   C10  116.33  3.000
 Y47  C9   N3   C10  119.49  3.000
 Y47  H5   C4   C3   127.40  3.000
 Y47  H5   C4   C5   126.33  3.000
 Y47  C3   C4   C5   106.27  3.000
 Y47  O3   C5   C6   121.38  3.000
 Y47  O3   C5   C4   109.51  3.000
 Y47  C6   C5   C4   128.93  3.000
 Y47  O1   C6   C5   118.11  3.000
 Y47  O1   C6   N1   122.79  3.000
 Y47  C5   C6   N1   119.09  3.000
 Y47  H7   C7   H6   107.86  3.000
 Y47  H7   C7   C8   109.12  3.000
 Y47  H6   C7   C8   109.78  3.000
 Y47  H7   C7   N1   110.39  3.000
 Y47  H6   C7   N1   109.59  3.000
 Y47  C8   C7   N1   110.06  3.000
 Y47  H8   C8   H9   107.99  3.000
 Y47  H8   C8   N2   111.24  3.000
 Y47  H9   C8   N2   110.48  3.000
 Y47  H8   C8   C7   109.32  3.000
 Y47  H9   C8   C7   106.13  3.000
 Y47  N2   C8   C7   111.49  3.000
 Y47  H12  C10  H11  106.38  3.000
 Y47  H12  C10  C11  109.62  3.000
 Y47  H11  C10  C11  109.62  3.000
 Y47  H12  C10  N3   106.77  3.000
 Y47  H11  C10  N3   110.28  3.000
 Y47  C11  C10  N3   113.86  3.000
 Y47  H14  C13  C14  120.35  3.000
 Y47  H14  C13  C12  121.21  3.000
 Y47  C14  C13  C12  118.44  3.000
 Y47  H16  C15  N4   116.02  3.000
 Y47  H16  C15  C11  119.92  3.000
 Y47  N4   C15  C11  124.06  3.000
 Y47  H19  C17  H20  106.91  3.000
 Y47  H19  C17  C16  110.01  3.000
 Y47  H20  C17  C16  109.49  3.000
 Y47  H19  C17  N1   112.23  3.000
 Y47  H20  C17  N1   107.86  3.000
 Y47  C16  C17  N1   110.23  3.000
 Y47  C12  C11  C15  117.16  3.000
 Y47  C15  C11  C10  120.88  3.000
 Y47  C12  C11  C10  121.95  3.000
 Y47  H13  C12  C11  120.14  3.000
 Y47  H13  C12  C13  120.42  3.000
 Y47  C11  C12  C13  119.44  3.000
 Y47  H15  C14  N4   116.62  3.000
 Y47  H15  C14  C13  120.40  3.000
 Y47  N4   C14  C13  122.98  3.000
 Y47  H18  C16  H17  107.86  3.000
 Y47  H18  C16  N2   110.65  3.000
 Y47  H17  C16  N2   109.26  3.000
 Y47  H18  C16  C17  109.35  3.000
 Y47  H17  C16  C17  109.04  3.000
 Y47  N2   C16  C17  110.62  3.000
 Y47  O3   C2   C3   109.52  3.000
 Y47  O3   C2   C1   117.58  3.000
 Y47  C3   C2   C1   132.89  3.000
 Y47  H4   C3   C2   126.07  3.000
 Y47  H4   C3   C4   127.41  3.000
 Y47  C2   C3   C4   106.52  3.000
 Y47  O2   C9   N2   121.83  3.000
 Y47  O2   C9   N3   120.69  3.000
 Y47  N2   C9   N3   117.45  3.000
 Y47  C9   N2   C16  117.06  3.000
 Y47  C16  N2   C8   115.23  3.000
 Y47  C9   N2   C8   122.96  3.000
 Y47  C14  N4   C15  117.93  3.000
 Y47  C2   O3   C5   108.17  3.000
 Y47  H1   C1   H2   108.08  3.000
 Y47  H1   C1   H3   107.63  3.000
 Y47  H2   C1   H3   108.04  3.000
 Y47  H1   C1   C2   111.67  3.000
 Y47  H2   C1   C2   109.68  3.000
 Y47  H3   C1   C2   111.62  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 Y47  CONST_01  O3   C2   C3   C4      0.00   0.0  0
 Y47  CONST_02  C2   O3   C5   C4      0.00   0.0  0
 Y47  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 Y47  CONST_04  C3   C2   O3   C5      0.00   0.0  0
 Y47  CONST_05  C15  C11  C12  C13     0.00   0.0  0
 Y47  CONST_06  C15  N4   C14  C13     0.00   0.0  0
 Y47  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 Y47  CONST_08  C14  N4   C15  C11     0.00   0.0  0
 Y47  CONST_09  N4   C15  C11  C12     0.00   0.0  0
 Y47  CONST_10  N4   C14  C13  C12     0.00   0.0  0
 Y47  CONST_11  O3   C5   C4   C3      0.00   0.0  0
 Y47  CONST_12  C1   C2   C3   C4    180.00   0.0  0
 Y47  CONST_13  C1   C2   O3   C5    180.00   0.0  0
 Y47  CONST_14  C3   C4   C5   C6    180.00   0.0  0
 Y47  CONST_15  C2   O3   C5   C6    180.00   0.0  0
 Y47  CONST_16  C13  C12  C11  C10   180.00   0.0  0
 Y47  CONST_17  N4   C15  C11  C10   180.00   0.0  0
 Y47  CONST_18  C7   N1   C6   C5    180.00   0.0  0
 Y47  CONST_20  H4   C3   C4   C5    180.00   0.0  0
 Y47  CONST_21  H15  C14  N4   C15   180.00   0.0  0
 Y47  CONST_22  H13  C12  C11  C15   180.00   0.0  0
 Y47  CONST_23  H14  C13  C12  C11   180.00   0.0  0
 Y47  CONST_24  H16  C15  C11  C12   180.00   0.0  0
 Y47  CONST_25  H5   C4   C3   C2    180.00   0.0  0
 Y47  CONST_26  O1   C6   N1   C7      0.00   0.0  0
 Y47  CONST_27  O2   C9   N2   C8    180.00   0.0  0
 Y47  CONST_30  C8   N2   C9   N3      0.00   0.0  0
 Y47  CONST_32  N2   C9   N3   C10   180.00   0.0  0
 Y47  CONST_34  O2   C9   N3   C10     0.00   0.0  0
 Y47  Var_01    N2   C8   C7   N1     52.54  30.0  1
 Y47  Var_02    N2   C16  C17  N1    -54.47  30.0  1
 Y47  Var_03    C16  C17  N1   C7     61.19  30.0  1
 Y47  Var_04    C16  N2   C8   C7    -48.95  30.0  1
 Y47  Var_05    C17  N1   C7   C8    -59.80  30.0  1
 Y47  Var_06    C17  C16  N2   C8     49.73  30.0  1
 Y47  Var_07    C4   C5   C6   N1   -156.34  30.0  2
 Y47  Var_08    C12  C11  C10  N3    131.03  30.0  2
 Y47  Var_09    H3   C1   C2   C3   -119.95  30.0  2
 Y47  Var_10    C9   N3   C10  C11   -66.76  30.0  1

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 Y47  plan-1  C4   0.020
 Y47  plan-1  C5   0.020
 Y47  plan-1  C6   0.020
 Y47  plan-1  C2   0.020
 Y47  plan-1  C3   0.020
 Y47  plan-1  O3   0.020
 Y47  plan-1  H5   0.020
 Y47  plan-1  H4   0.020
 Y47  plan-1  C1   0.020
 Y47  plan-2  C10  0.020
 Y47  plan-2  C13  0.020
 Y47  plan-2  C15  0.020
 Y47  plan-2  C11  0.020
 Y47  plan-2  C12  0.020
 Y47  plan-2  C14  0.020
 Y47  plan-2  N4   0.020
 Y47  plan-2  H14  0.020
 Y47  plan-2  H16  0.020
 Y47  plan-2  H13  0.020
 Y47  plan-2  H15  0.020
 Y47  plan-3  N3   0.020
 Y47  plan-3  C8   0.020
 Y47  plan-3  C10  0.020
 Y47  plan-3  C16  0.020
 Y47  plan-3  C9   0.020
 Y47  plan-3  N2   0.020
 Y47  plan-3  O2   0.020
 Y47  plan-3  H10  0.020
 Y47  plan-4  N1   0.020
 Y47  plan-4  C5   0.020
 Y47  plan-4  C6   0.020
 Y47  plan-4  C7   0.020
 Y47  plan-4  C17  0.020
 Y47  plan-4  O1   0.020

